17-3291829-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002550.3(OR3A1):c.754G>T(p.Ala252Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002550.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR3A1 | NM_002550.3 | c.754G>T | p.Ala252Ser | missense_variant | 2/2 | ENST00000323404.2 | NP_002541.2 | |
OR3A2 | NM_002551.5 | c.-278-7278G>T | intron_variant | NP_002542.4 | ||||
OR3A2 | XM_047436157.1 | c.-255+7277G>T | intron_variant | XP_047292113.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR3A1 | ENST00000323404.2 | c.754G>T | p.Ala252Ser | missense_variant | 2/2 | 6 | NM_002550.3 | ENSP00000313803.1 | ||
OR3A2 | ENST00000573901.3 | c.-278-7278G>T | intron_variant | 3 | ENSP00000516654.1 | |||||
OR3A2 | ENST00000573491.5 | c.-84-12676G>T | intron_variant | 3 | ENSP00000493118.1 | |||||
OR3A2 | ENST00000576166.2 | c.-84-12676G>T | intron_variant | 5 | ENSP00000493095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251360Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135838
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461520Hom.: 0 Cov.: 30 AF XY: 0.0000578 AC XY: 42AN XY: 726974
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.754G>T (p.A252S) alteration is located in exon 1 (coding exon 1) of the OR3A1 gene. This alteration results from a G to T substitution at nucleotide position 754, causing the alanine (A) at amino acid position 252 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at